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For the Filling:
8 oz. cream cheese, at room temperature
1/3 cup granulated sugar
1 large egg, at room temperature
2 oz. bittersweet chocolate, coarsely chopped
For the Cupcakes:
1½ cups all-purpose flour
1 cup firmly packed light brown sugar
5 tablespoons naturally unsweetened cocoa powder (not Dutch-process)
1 teaspoon baking soda
¼ teaspoon salt
1 cup water
1/3 cup unflavored vegetable oil
1 tablespoon white vinegar
1 teaspoon vanilla extract
Directions for the Black-Bottom Cupcakes
1. To make the Filling: Beat together the cream cheese, granulated sugar, and egg until smooth. Stir in chopped chocolate pieces. Set aside.
2. To make the Cupcakes: Adjust the rack to the center of the oven and preheat to 350°F (175°C). Butter a 12-cup muffin tin, or line the tin with paper muffin cups.
3. In a medium bowl sift together the flour, brown sugar, cocoa powder, baking soda, and salt. In a separate bowl mix together the water, oil, vinegar, and vanilla.
4. Make a well in the center of the dry ingredients and stir in the wet ingredients, stirring just until smooth. Stir any longer and you will over mix the batter and end up with less-than-tender cupcakes.
5. Divide the batter among the muffin cups. Spoon a few tablespoons of the filling into the center of each cupcake, dividing the filling evenly. This will fill the cups almost completely, which is fine.
6. Bake for 25 minutes, or until the tops are slightly golden brown and the cupcakes feel springy when gently pressed. These moist treats will keep unrefrigerated for 2 to 3 days if stored in an airtight container.